The study of stem cells promises to yield important insights into a broad range of human diseases including cancer and organ failure. Furthermore, the regenerative potential of stem cells makes them ideal candidates for therapeutic applications. Emerging evidence suggests chromatin organization plays a pivotal role in establishing stem cell identity and maintenance. Our long-term goal is to identify and characterize the molecules responsible for gene regulation in stem cells. As a model, we study two different types of stem cells in adult Drosophila, the germline stem cells of the ovary and the intestinal stem cells of the adult midgut. We have focused our initial efforts on characterizing the Drosophila scrawny (scny) gene. SCNY first captured our attention because it is a conserved ubiquitin specific protease that deubiquitylates histone H2B and functions in gene silencing. Our genetic analysis showed that disruption of scny results in stem cell loss in multiple tissues. In this proposal we build upon these preliminary findings. In Aim 1, we seek to define what cells require scny function using a number of genetic approaches. In Aim 2, we genetically and biochemically define the domain structure of the SCNY protein. In Aim 3, we test if SCNY directly regulates the expression of candidate genes. Finally, in Aim 4 we characterize the function of PAF1 and two histone H2B ubiquitin ligases and test whether they interact with scny. This work will illuminate our understanding of scny function. Given the conservation of the histone modification hierarchy, principles revealed under this proposal will provide a basis for understanding the intrinsic programs of mammalian stem cells in both normal and diseased states. PUBLIC HEALTH RELEVANCE: The study and clinical use of stem cells is poised to have a profound impact on medical science. This proposal focuses on understanding the unique mechanisms that control gene expression in stem cells using Drosophila as a model system. We believe this work will reveal fundamental principles in stem cell biology and thus will accelerate the use of these cells in the treatment of human diseases.